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Feature #493

closed

Ed's iteration alignment

Added by Anke Mulder almost 14 years ago. Updated over 13 years ago.

Status:
Closed
Priority:
High
Assignee:
Anchi Cheng
Category:
-
Target version:
Appion/Leginon 2.2.0
Start date:
05/17/2010
Due date:
% Done:

100%

Estimated time:

Description

Default values for last ring radius and par bin are not set.

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 #1

Updated by Neil Voss almost 14 years ago

  • Project changed from 5 to Appion
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 #2

Updated by Neil Voss almost 14 years ago

  • Target version set to Appion/Leginon 2.0.0
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 #3

Updated by Anke Mulder almost 14 years ago

  • Assignee set to Ed Brignole
  • Priority changed from Normal to Immediate
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 #4

Updated by Neil Voss almost 14 years ago

  • Status changed from New to Assigned
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 #5

Updated by Amber Herold almost 14 years ago

  • Target version changed from Appion/Leginon 2.0.0 to Appion/Leginon 2.0.1
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 #6

Updated by Ed Brignole almost 14 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Ed Brignole to Neil Voss

changed code in /home/brignole/myami/myamiweb/processing/runEdIterAlignment.php

How can I test the changes made to the code before committing them?

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 #7

Updated by Neil Voss almost 14 years ago

  • Assignee changed from Neil Voss to Ed Brignole

Ed, you have to commit the code and to tell me what the subversion revision number it is. Also to make it easier in the svn commit message add the text 'refs #493' and redmine will automatically link the svn commit to this bug.

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 #8

Updated by Ed Brignole almost 14 years ago

So then what do I do if it chokes while committing! see below:

Sending processing/runEdIterAlignment.php
Authentication realm: <http://ami:80> AMI Realm
Password for 'brignole':
svn: Commit failed (details follow):
svn: CHECKOUT of '/svn/myami/!svn/ver/14118/trunk/myamiweb/processing/runEdIterAlignment.php': 403 Forbidden (http://ami)
svn: Your commit message was left in a temporary file:
svn: '/home/brignole/myami/myamiweb/processing/svn-commit.tmp'

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 #9

Updated by Neil Voss almost 14 years ago

I would checkout it again:

svn --username=brignole co http://emg.nysbc.org/svn/myami/trunk/ myami-new/
cp -v myami/myamiweb/processing/runEdIterAlignment.php myami-new/myamiweb/processing/runEdIterAlignment.php
svn commit myami-new/myamiweb/processing/runEdIterAlignment.php
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 #10

Updated by Ed Brignole almost 14 years ago

  • Status changed from In Code Review to In Test
  • Assignee changed from Ed Brignole to Anke Mulder

Bin and last ring are set on web page. #freealigns changed to 1.

Changes to runEdIterAlignment.php were committed to trunk and branches.

Christopher fixed my permissions so I can commit changes. Then went through setup wizard so I can see changes to web pages at http://fly/~brignole/myami/myamiweb

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 #11

Updated by Anke Mulder almost 14 years ago

  • Status changed from In Test to Closed

the params are set

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 #12

Updated by Anke Mulder almost 14 years ago

  • Status changed from Closed to Assigned

The default values are set, but the program now does not complete.

End of log file:

Traceback (most recent call last):
File "/opt/appion/bin/edIterAlign.py", line 551, in ?
edIterAlign.start()
File "/opt/appion/bin/edIterAlign.py", line 513, in start
self.runSpiderBatch( batchfilepath, spiderstack )
File "/opt/appion/bin/edIterAlign.py", line 472, in runSpiderBatch
apDisplay.printError("Doc file, apshdoc.spi does not exist.")
File "/var/tmp/appion-2.0-6_rc1-root/opt/appion/appionlib/apDisplay.py", line 56, in printError
Exception:
  • FATAL ERROR ***
    Doc file, apshdoc.spi does not exist.
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 #13

Updated by Anke Mulder almost 14 years ago

  • Assignee changed from Anke Mulder to Ed Brignole
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 #14

Updated by Ed Brignole almost 14 years ago

  • Status changed from Assigned to In Test
  • Assignee changed from Ed Brignole to Anke Mulder

Problem was incompatibility of old spider scripts with new Spider18.

1) Deleted old spiderbatch directory, replaced with new spiderbatch directory and the handfull of necessary scripts that are compatible with Spider18 .

2) Updated edIterAlign.py and runEdIterAlignment.php for new spider batch script.

3) Removed option to set number of free-alignments, now set permanently to 1 for faster and better results. --freealigns flag no longer permitted

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 #15

Updated by Neil Voss almost 14 years ago

  • Target version changed from Appion/Leginon 2.0.1 to Appion/Leginon 2.1.0
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 #16

Updated by Neil Voss almost 14 years ago

  • Target version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.0.2
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 #17

Updated by Amber Herold almost 14 years ago

  • Assignee changed from Anke Mulder to Anchi Cheng
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 #18

Updated by Amber Herold almost 14 years ago

  • Status changed from In Test to Closed
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 #19

Updated by Amber Herold almost 14 years ago

  • Status changed from Closed to In Test
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 #20

Updated by Anchi Cheng almost 14 years ago

  • Status changed from In Test to Assigned
  • Assignee changed from Anchi Cheng to Neil Voss

tested since Anke is not here.

ran on amibox02

appion edIterAlign.py --projectid=5 --rundir=/ami/data00/appion/10may07o04/align/editer4 --runname=editer4 --description="test" --templates=303,301 --orientref=303 --stack=1300 --nparticles=44 --bin=3 --radius=47 --lowpass=10 --highpass=2000 --iterations=10 --commit

executing command: ('/ami/data00/appion/10may07o04/align/editer4/IterativeClassifyAlign',)
.OPERATION: /ami/data00/appion/10may07o04/align/editer4/IterativeClassifyAlign
Traceback (most recent call last):
File "/ami/sw/leginon/myami-trunk/appion/bin/edIterAlign.py", line 558, in ?
edIterAlign.start()
File "/ami/sw/leginon/myami-trunk/appion/bin/edIterAlign.py", line 520, in start
self.runSpiderBatch( batchfilepath, spiderstack )
File "/ami/sw/leginon/myami-trunk/appion/bin/edIterAlign.py", line 479, in runSpiderBatch
apDisplay.printError("Output alignment parameters file apshdoc.spi does not exist.")
File "/ami/sw/leginon/myami-trunk/appion/appionlib/apDisplay.py", line 56, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception: * FATAL ERROR *
Output alignment parameters file apshdoc.spi does not exist.

Tried my trunk co and got the same result.
I don't not know what output would be reasonable, though.

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 #21

Updated by Neil Voss almost 14 years ago

  • Assignee changed from Neil Voss to Ed Brignole
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 #22

Updated by Neil Voss almost 14 years ago

  • Target version changed from Appion/Leginon 2.0.2 to Appion/Leginon 2.1.0

Moving to 2.1 release too unstable for the branch.

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 #23

Updated by Ed Brignole almost 14 years ago

I just tested on amibox02 and it runs fine.
/home/brignole/ami_html/myami/appion/bin/edIterAlign.py \
--projectid=118 --rundir=/ami/data00/appion/10may28d/align/editer_test1 \
--runname=editer_test1 --description=test --templates=366,354,349 \
--orientref=366 --stack=1499 --nparticles=50 --bin=2 --radius=46 \
--lowpass=10 --highpass=2000 --iterations=2 --commit

Your run crashed during the first iteration while orienting the class averages to your reference image. However, since we terminate the spider results file it's hard to say exactly which command spider choked on. Can you see if the run that worked for me will run for you with different runname?

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 #24

Updated by Amber Herold almost 14 years ago

  • Target version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.2.0
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 #25

Updated by Amber Herold over 13 years ago

  • Assignee changed from Ed Brignole to Anchi Cheng
  • Priority changed from Immediate to High

Anchi, it looks like we need you to try this one more time...

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 #26

Updated by Anchi Cheng over 13 years ago

  • Status changed from Assigned to Closed
  • % Done changed from 0 to 100

It worked with Ed's stack but not the script and session I had posted before. Probably because I didn't invert the template.

This one does work:

edIterAlign.py --projectid=5 --rundir=/ami/data15/appion/10may07o04/align/editer5 --runname=editer5 --description="test ed iter" --templates=277,276 --orientref=303 --stack=1298 --nparticles=50 --bin=2 --radius=170 --lowpass=10 --highpass=2000 --iterations=2 --invert-templates --commit

The result gives good orientation alignment but not shift because the original stack was not centered on particles.

As a feature, this is closed.

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